Identifying polymorphisms in the Alzheimer's related APP gene using the MinION sequencer

Brookes, Keeley (2016) Identifying polymorphisms in the Alzheimer's related APP gene using the MinION sequencer. Journal of Next Generation Sequencing & Applications, 3 (1). ISSN 2469-9853

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The MinION is a bench top sequencer by Oxford nanopore technologies (ONT) that allows long reads of DNA sequence. Few studies have tested whether polymorphisms can be detected using this device. Several polymorphisms within the APP gene were used to test this capability. Library preparation and sequencing were performed using standard ONT protocols for samples harbouring ive different mutations. Alignments to the reference sequence were analysed in MinoTour and basecalls were manually investigated using proportion of reference calls between samples to identify the variants. MinoTour’s algorithm for variant detection was unable to identify the polymorphisms due to high base calling error rate. By calculating the difference in reference basecall proportions along the amplicon, it was possible to identify the polymorphisms above a Bonferroni-corrected threshold (p<1 × 10-4). The MinION has potential for polymorphism detection when comparing samples; however careful interpretation is needed as high base calling error rates can mask the presence of polymorphisms.

Item Type: Article
Keywords: Nanopore technology; MinION; Sequencing; Polymorphism detection; Deletion
Schools/Departments: University of Nottingham UK Campus > Faculty of Medicine and Health Sciences > School of Life Sciences > School of Molecular Medical Sciences > Human Genetics Research Group
Identification Number:
Depositing User: Morgan, Kevin
Date Deposited: 27 May 2016 08:49
Last Modified: 15 Sep 2016 22:06

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